BtaINT0122366 @ bosTau6
Intron Retention
Gene
ENSBTAG00000006828 | RAPGEF3
Description
Rap guanine nucleotide exchange factor (GEF) 3 [Source:HGNC Symbol;Acc:HGNC:16629]
Coordinates
chr5:32705646-32706034:+
Coord C1 exon
chr5:32705646-32705722
Coord A exon
chr5:32705723-32705887
Coord C2 exon
chr5:32705888-32706034
Length
165 bp
Sequences
Splice sites
5' ss Seq
AAGGTGAGT
5' ss Score
10.47
3' ss Seq
TAACTCGGGCCTGGCTGCAGGGC
3' ss Score
4.38
Exon sequences
Seq C1 exon
TGTTCAGCCAGGGGGACAAGGGCACCTCGTGGTACATTATCTGGAAGGGATCGGTCAACGTGGTGACCCATGGCAAG
Seq A exon
GTGAGTCTTCCCCCATGCCCAGCCCCTGGGCAGAGCTGGTCTCTGGTCCTTGTCCTTTAATGGACCCAAGGCTGCTGGCCTCTCAGGTCTCCTCCTGCTTTGGTGGCTCTGGGTCTGTCCCGGTGAGGGCTGGGGGGCTGGGCTGTAACTCGGGCCTGGCTGCAG
Seq C2 exon
GGCCTGGTGACCACCCTGCACGAGGGAGATGACTTCGGACAGCTGGCTCTGGTGAACGATGCACCTCGGGCCGCCACCATCATCCTGGGAGAAGACAACTGTCATTTTCTTCGTGTGGACAAGCAGGACTTCAACCGTATCATCAAG
VastDB Features
Vast-tools module Information
Secondary ID
ENSBTAG00000006828:ENSBTAT00000008976:9
Average complexity
IR
Mappability confidence:
NA
Protein Impact
ORF disruption upon sequence inclusion
No structure available
Features
Disorder rate (Iupred):
C1=0.000 A=NA C2=0.000
Domain overlap (PFAM):
C1:
PF0002724=cNMP_binding=FE(29.4=100)
A:
NA
C2:
PF0002724=cNMP_binding=FE(56.5=100)
Main Inclusion Isoform:
NA
Other Inclusion Isoforms:
NA
Other Skipping Isoforms:
NA
Associated events
Conservation
Fruitfly
(dm6)
No conservation detected
Primers PCR
Suggestions for RT-PCR validation
F:
TGTTCAGCCAGGGGGACAAG
R:
TGATACGGTTGAAGTCCTGCT
Band lengths:
219-384
Functional annotations
There are 0 annotated functions for this event
GENOMIC CONTEXT[edit]
INCLUSION PATTERN[edit]